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Bähr S, Simonneau A, Irran E, Oestreich M. An Air-Stable Dimeric Ru–S Complex with an NHC as Ancillary Ligand for Cooperative Si–H Bond Activation. Organometallics 2016. [DOI: 10.1021/acs.organomet.6b00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Susanne Bähr
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Antoine Simonneau
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Elisabeth Irran
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 115, 10623 Berlin, Germany
| | - Martin Oestreich
- Institut für Chemie, Technische Universität Berlin, Strasse des 17. Juni 115, 10623 Berlin, Germany
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2
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Hartmann E, Hammer MM, Gschwind RM. Structures and interligand interaction pattern of phosphoramidite Pd complexes by NMR spectroscopy: modulations in extended interaction surfaces as stereoselection mode of a privileged class of ligands. Chemistry 2013; 19:10551-62. [PMID: 23794174 DOI: 10.1002/chem.201300095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Indexed: 11/10/2022]
Abstract
During the last decade, phosphoramidites have been established as a so-called privileged class of ligands in various transition metal catalyses. However, the interactions responsible for their favorable properties have hitherto remained elusive. To address this issue, the formation trends, structural features, and interligand interaction patterns of several trans- and cis-[PdLL'Cl2] complexes have been investigated by NMR spectroscopy. The energetic contribution of their interligand interactions has been measured experimentally using the supramolecular balance for transition-metal complexes. The resulting energetics combined with an analysis of the electrostatic potential surfaces reveal that in phosphoramidites not only the aryl groups but the complete (CH)CH3 Ph moieties of the amine side chains form extended quasi-planar CH-π and π-π interaction surfaces. Application of the supramolecular balance has shown that modulations in these extended interaction surfaces cause energetic differences that are relevant to enantioselective catalysis. In addition, the energetics of these interligand interactions are quite independent of the actual structures of the complexes. This is shown by similar formation and aggregation trends of complexes with the same ligand but different structures. The extended quasi-planar electrostatic interaction surface of the (CH)CH3 Ph moiety explains the known pattern of successful ligand modulation and the substrate specificity of phosphoramidites. Thus, we propose modulations in these extended CH-π and π-π interaction areas as a refined stereoselection mode for these ligands. Based on the example of phosphoramidites, this study reveals three general features potentially applicable to various ligands in asymmetric catalysis. First, specific combinations of alkyl and aryl moieties can be used to create extended anisotropic interaction areas. Second, modulations in these interaction surfaces cause energetic differences that are relevant to catalytic applications. Third, bulky substituents with matching complementary interaction surfaces should not only be considered in terms of steric hindrance but also in terms of attractive and repulsive interactions, a feature that may often be underestimated in asymmetric catalysis.
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Affiliation(s)
- Evelyn Hartmann
- Institut für Organische Chemie, Universität Regensburg, Universitätsstr. 31, 93040 Regensburg, Germany
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3
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Li CY, Liu DC, Ko BT. Synthesis, characterization and reactivity of single-site aluminium amides bearing benzotriazole phenoxide ligands: catalysis for ring-opening polymerization of lactide and carbon dioxide/propylene oxide coupling. Dalton Trans 2013; 42:11488-96. [DOI: 10.1039/c3dt51003d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Chen-Yu Li
- Department of Chemistry, Chung Yuan Christian University, Chung-Li 320, Taiwan
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Tanabe M, Yumoto R, Osakada K, Sanji T, Tanaka M. Preparation and Properties of Perarylated 3,4-Disila-1,5-hexadienes. A Fluorescent Disilane Accommodated in the Crystal Lattice. Organometallics 2012. [DOI: 10.1021/om300551t] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makoto Tanabe
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-3 Nagatsuta, Midori-ku, Yokohama
226-8503, Japan
| | - Ryouhei Yumoto
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-3 Nagatsuta, Midori-ku, Yokohama
226-8503, Japan
| | - Kohtaro Osakada
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-3 Nagatsuta, Midori-ku, Yokohama
226-8503, Japan
| | - Takanobu Sanji
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-3 Nagatsuta, Midori-ku, Yokohama
226-8503, Japan
| | - Masato Tanaka
- Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-3 Nagatsuta, Midori-ku, Yokohama
226-8503, Japan
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5
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Vargiu AV, Magistrato A. Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study. Inorg Chem 2012; 51:2046-57. [DOI: 10.1021/ic201659v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Attilio V. Vargiu
- CNR-IOM, Unità Operativa
di Supporto SLACS, c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato,
Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos,
National
Simulation Center, c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste,
Italy
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6
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Zhao Q, Liu XM, Song WC, Bu XH. Valence-induced assembly of CuI–CuII ions into different discrete coordination architectures by a disk-shaped polypyridyl ligand. Dalton Trans 2012; 41:6683-8. [DOI: 10.1039/c2dt00002d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Sgrignani J, Franco D, Magistrato A. Theoretical studies of homogeneous catalysts mimicking nitrogenase. Molecules 2011; 16:442-65. [PMID: 21221062 PMCID: PMC6259282 DOI: 10.3390/molecules16010442] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/27/2010] [Accepted: 01/05/2011] [Indexed: 11/16/2022] Open
Abstract
The conversion of molecular nitrogen to ammonia is a key biological and chemical process and represents one of the most challenging topics in chemistry and biology. In Nature the Mo-containing nitrogenase enzymes perform nitrogen 'fixation' via an iron molybdenum cofactor (FeMo-co) under ambient conditions. In contrast, industrially, the Haber-Bosch process reduces molecular nitrogen and hydrogen to ammonia with a heterogeneous iron catalyst under drastic conditions of temperature and pressure. This process accounts for the production of millions of tons of nitrogen compounds used for agricultural and industrial purposes, but the high temperature and pressure required result in a large energy loss, leading to several economic and environmental issues. During the last 40 years many attempts have been made to synthesize simple homogeneous catalysts that can activate dinitrogen under the same mild conditions of the nitrogenase enzymes. Several compounds, almost all containing transition metals, have been shown to bind and activate N₂ to various degrees. However, to date Mo(N₂)(HIPTN)₃N with (HIPTN)₃N= hexaisopropyl-terphenyl-triamidoamine is the only compound performing this process catalytically. In this review we describe how Density Functional Theory calculations have been of help in elucidating the reaction mechanisms of the inorganic compounds that activate or fix N₂. These studies provided important insights that rationalize and complement the experimental findings about the reaction mechanisms of known catalysts, predicting the reactivity of new potential catalysts and helping in tailoring new efficient catalytic compounds.
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Affiliation(s)
- Jacopo Sgrignani
- CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy
| | - Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS National Simulation Center at SISSA, via Bonomea 265, Trieste, Italy
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8
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Tsai CY, Li CY, Lin CH, Huang BH, Ko BT. Reactions of 4-methylidene-bis(1-phenyl-3-methylpyrazol-5-one) with trimethylaluminum: Synthesis, structure and catalysis for the ring-opening polymerization of ε-caprolactone. INORG CHEM COMMUN 2011. [DOI: 10.1016/j.inoche.2010.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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9
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Li CY, Tsai CY, Lin CH, Ko BT. Synthesis, structural characterization and reactivity of aluminium complexes supported by benzotriazole phenoxide ligands: air-stable alumoxane as an efficient catalyst for ring-opening polymerization of l-lactide. Dalton Trans 2011; 40:1880-7. [DOI: 10.1039/c0dt01108h] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Albinati A, Macchioni A. Preface. Inorganica Chim Acta 2010. [DOI: 10.1016/j.ica.2009.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Skarżyńska A, Siczek M. Reactivity of oxo-rhenium precursor trans-ReOCl3(OPPh3)(SMe2) with diaza heterocyclic congeners: Synthesis and spectroscopic characterization of mono and dinuclear compounds. Polyhedron 2008. [DOI: 10.1016/j.poly.2008.02.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Spiegel K, Magistrato A, Maurer P, Ruggerone P, Rothlisberger U, Carloni P, Reedijk J, Klein ML. Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. J Comput Chem 2008; 29:38-49. [PMID: 17705162 DOI: 10.1002/jcc.20739] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Azole-bridged diplatinum compounds are promising new anticancer drugs designed to induce small distortions upon DNA alkylation, able to circumvent resistance problems of existing platinum drugs. Hybrid quantum classical (QM/MM) molecular dynamics (MD) simulations of different azole-bridged platinum drugs have recently revealed the nature of the local deformations at the DNA binding site. However, the description of global slow converging rearrangements cannot be addressed by QM/MM MD due to the short time scale accessible. Extensive classical MD simulations are therefore mandatory to describe accurately the structural distortions in the DNA double helix. This issue is now addressed by developing a new set of accurate force field parameters of the platinated moiety via a recently proposed force matching procedure of the classical forces to ab initio forces obtained from QM/MM trajectories. The accuracy of our force field parameters is validated by comparison of structural properties from classical MD and hybrid QM/MM simulations. The structural characteristics of the Pt-lesion are well reproduced during classical MD compared with QM/MM simulations and available experimental data. The global distortions in the DNA duplex upon binding of dinuclear Pt-compounds are very small and rather opposite to those induced by cisplatin. Thus, the force match approach significantly extends the potentialities of molecular simulations in the study of anticancer drugs and of the interactions with their biological targets.
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Affiliation(s)
- Katrin Spiegel
- Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.
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13
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Moldovan N, Lönnecke P, Silaghi-Dumitrescu I, Silaghi-Dumitrescu L, Hey-Hawkins E. Palladium(II) and Platinum(II) Complexes with Heteroditopic 10-(Aryl)phenoxarsine (Aryl = 2-C6H4OR, R = H, Me, Pri) Ligands: Solvent-Oriented Crystallization of cis Isomers. Inorg Chem 2008; 47:1524-31. [DOI: 10.1021/ic7021648] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Natalia Moldovan
- Department of Chemistry, Babes-Bolyai University, Kogalniceanu 1, RO-400084, Cluj-Napoca,
- Romania and Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, D-04103, Leipzig, Germany
| | - Peter Lönnecke
- Department of Chemistry, Babes-Bolyai University, Kogalniceanu 1, RO-400084, Cluj-Napoca,
- Romania and Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, D-04103, Leipzig, Germany
| | - Ioan Silaghi-Dumitrescu
- Department of Chemistry, Babes-Bolyai University, Kogalniceanu 1, RO-400084, Cluj-Napoca,
- Romania and Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, D-04103, Leipzig, Germany
| | - Luminita Silaghi-Dumitrescu
- Department of Chemistry, Babes-Bolyai University, Kogalniceanu 1, RO-400084, Cluj-Napoca,
- Romania and Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, D-04103, Leipzig, Germany
| | - Evamarie Hey-Hawkins
- Department of Chemistry, Babes-Bolyai University, Kogalniceanu 1, RO-400084, Cluj-Napoca,
- Romania and Universität Leipzig, Institut für Anorganische Chemie, Johannisallee 29, D-04103, Leipzig, Germany
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14
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Nama D, Schott D, Pregosin PS, Veiros LF, Calhorda MJ. Diffusion and Overhauser NMR Studies on Dicationic Palladium Complexes of BINAP. Organometallics 2006. [DOI: 10.1021/om0603518] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Devendrababu Nama
- Laboratory of Inorganic Chemistry, ETH, Zürich, CH-8093 Switzerland, Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Daniele Schott
- Laboratory of Inorganic Chemistry, ETH, Zürich, CH-8093 Switzerland, Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Paul S. Pregosin
- Laboratory of Inorganic Chemistry, ETH, Zürich, CH-8093 Switzerland, Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - L. F. Veiros
- Laboratory of Inorganic Chemistry, ETH, Zürich, CH-8093 Switzerland, Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - M. J. Calhorda
- Laboratory of Inorganic Chemistry, ETH, Zürich, CH-8093 Switzerland, Centro de Química Estrutural, Complexo I, Instituto Superior Técnico, Avenida Rovisco Pais 1, 1049-001 Lisbon, Portugal, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
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15
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Mercuri F, Sgamellotti A. Functionalization of Carbon Nanotubes with Vaska's Complex: A Theoretical Approach. J Phys Chem B 2006; 110:15291-4. [PMID: 16884247 DOI: 10.1021/jp060929r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The functionalization of single-walled carbon nanotubes (CNTs) with Vaska's complex trans-Ir(CO)Br(PPh(3))(2) has been investigated by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. The formation of a stable adduct has been experimentally evidenced by Wong et al. (Nano Lett. 2002, 2, 49), but microscopical details on the metal-nanotube interaction are still unclear. Our calculations show a low propensity to eta(2) coordination of Vaska's complex with the perfect hexagonal network of CNTs. Rather, a stronger interaction takes place when the transition metal center coordinates to carbon atoms belonging to pentagonal rings, as in topological defects or end-caps.
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Affiliation(s)
- Francesco Mercuri
- ISTM-CNR and Dipartimento di Chimica, Università di Perugia, I-06123 Perugia, Italy
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16
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Landis CR, Nelson RC, Jin W, Bowman AC. Synthesis, Characterization, and Transition-Metal Complexes of 3,4-Diazaphospholanes. Organometallics 2006. [DOI: 10.1021/om050922g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clark R. Landis
- Department of Chemistry, University of WisconsinMadison, 1101 University of Ave., Madison, Wisconsin 53706
| | - Ryan C. Nelson
- Department of Chemistry, University of WisconsinMadison, 1101 University of Ave., Madison, Wisconsin 53706
| | - Wiechang Jin
- Department of Chemistry, University of WisconsinMadison, 1101 University of Ave., Madison, Wisconsin 53706
| | - Amanda C. Bowman
- Department of Chemistry, University of WisconsinMadison, 1101 University of Ave., Madison, Wisconsin 53706
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17
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Magistrato A, Togni A, Rothlisberger U. Enantioselective Palladium-Catalyzed Hydrosilylation of Styrene: Influence of Electronic and Steric Effects on Enantioselectivity and Catalyst Design via Hybrid QM/MM Molecular Dynamics Simulations. Organometallics 2006. [DOI: 10.1021/om050246i] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alessandra Magistrato
- CNR-INFM-Democritos National Simulation Center and International School for Advanced Studies (SISSA/ISAS), via Beirut 2-4, Trieste, Italy, Department of Chemistry and Applied Biosciences, ETH-Hoenggerberg, HCI, CH-8093 Zürich, Switzerland, and Laboratory of Molecular Chemistry and Biology, EPFL, CH-1015 Lausanne, Switzerland
| | - Antonio Togni
- CNR-INFM-Democritos National Simulation Center and International School for Advanced Studies (SISSA/ISAS), via Beirut 2-4, Trieste, Italy, Department of Chemistry and Applied Biosciences, ETH-Hoenggerberg, HCI, CH-8093 Zürich, Switzerland, and Laboratory of Molecular Chemistry and Biology, EPFL, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- CNR-INFM-Democritos National Simulation Center and International School for Advanced Studies (SISSA/ISAS), via Beirut 2-4, Trieste, Italy, Department of Chemistry and Applied Biosciences, ETH-Hoenggerberg, HCI, CH-8093 Zürich, Switzerland, and Laboratory of Molecular Chemistry and Biology, EPFL, CH-1015 Lausanne, Switzerland
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18
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Hugosson HW, Laio A, Maurer P, Rothlisberger U. A comparative theoretical study of dipeptide solvation in water. J Comput Chem 2006; 27:672-84. [PMID: 16477697 DOI: 10.1002/jcc.20360] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water. Hybrid quantum mechanical/molecular mechanical simulations successfully reproduce the solvation patterns from the fully quantum mechanical simulations (PACS numbers: 87.14.Ee, 87.15.Aa, 87.15.He, 71.15.Pd).
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Affiliation(s)
- Håkan W Hugosson
- Laboratory of Computational Chemistry and Biochemistry, Institute of Molecular and Biological Chemistry, Swiss Federal Institute of Technology EPF Lausanne, Switzerland.
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19
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Jin Y, Lah MS. Polymorphism Driven by π-π Stacking and van der Waals Interactions: Preparation and Characterization of Polymorphic Vanadium Crystals of [VVO(Hacshz)(OEt)] and [VIV(Hacshz)2]. Eur J Inorg Chem 2005. [DOI: 10.1002/ejic.200500222] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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20
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Pu J, Gao J, Truhlar DG. Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. Chemphyschem 2005; 6:1853-65. [PMID: 16086343 PMCID: PMC4481131 DOI: 10.1002/cphc.200400602] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Indexed: 11/06/2022]
Abstract
The generalized hybrid orbital (GHO) method has previously been formulated for combining molecular mechanics with various levels of quantum mechanics, in particular semiempirical neglect of diatomic differential overlap theory, ab initio Hartree-Fock theory, and self-consistent charge density functional tight-binding theory. To include electron-correlation effects accurately and efficiently in GHO calculations, we extend the GHO method to density functional theory in the generalized-gradient approximation and hybrid density functional theory (denoted by GHO-DFT and GHO-HDFT, respectively) using Gaussian-type orbitals as basis functions. In the proposed GHO-(H)DFT formalism, charge densities in auxiliary hybrid orbitals are included to calculate the total electron density. The orthonormality constraints involving the auxiliary Kohn-Sham orbitals are satisfied by carrying out the hybridization in terms of a set of Löwdin symmetrically orthogonalized atomic basis functions. Analytical gradients are formulated for GHO-(H)DFT by incorporating additional forces associated with GHO basis transformations. Scaling parameters are introduced for some of the one-electron integrals and are optimized to obtain the correct charges and geometry near the QM/MM boundary region. The GHO-(H)DFT method based on the generalized gradient approach (GGA) (BLYP and mPWPW91) and HDFT methods (B3 LYP, mPW1PW91, and MPW1 K) is tested-for geometries and atomic charges-against a set of small molecules. The following quantities are tested: 1) the C--C stretch potential in ethane, 2) the torsional barrier for internal rotation around the central C--C bond in n-butane, 3) proton affinities for a set of alcohols, amines, thiols, and acids, 4) the conformational energies of alanine dipeptide, and 5) the barrier height of the hydrogen-atom transfer between n-C4H10 and n-C4H9, where the reaction center is described at the MPW1 K/6-31G(d) level of theory.
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Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E, Minneapolis, MN 55455–0431 (USA)
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Freindorf M, Shao Y, Furlani TR, Kong J. Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential. J Comput Chem 2005; 26:1270-8. [PMID: 15965971 DOI: 10.1002/jcc.20264] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.
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Affiliation(s)
- Marek Freindorf
- Center for Computational Research, The State University of New York at Buffalo, Buffalo, NY 14260, USA.
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22
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Gladiali S, Taras R, Ceder RM, Rocamora M, Muller G, Solans X, Font-Bardia M. Asymmetric allylic alkylation catalyzed by Pd(II)-complexes with (S)-BINPO, a hemilabile axially chiral P,O-heterodonor inducer. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Daura-Oller E, Segarra AM, Poblet JM, Claver C, Fernández E, Bo C. On the Origin of Regio- and Stereoselectivity in the Rhodium-Catalyzed Vinylarenes Hydroboration Reaction. J Org Chem 2004; 69:2669-80. [PMID: 15074912 DOI: 10.1021/jo035392h] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We studied the hydroboration of vinylarenes using rhodium complexes bearing atropoisomeric ligands. For the first time, an NMR spectroscopy study of the styrene and catecholborane addition to the precursor of catalyst [Rh(COD)(L-L)]BF(4), where L-L = (R)-BINAP and (R)-QUINAP, showed evidence of the structure of intermediates involved in the catalytic cycle. On the basis of this evidence, and using DFT calculations and QM/MM strategies, we investigated the origin of regio- and stereoselectivity. We determined the structure and stability of the key intermediates for several ligands and substrates and found excellent agreement between the relative stability of the intermediates and the experimentally observed trends. Using model systems, we analyzed the role of the steric and electronic features of the ligands and the substrates in detail.
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Affiliation(s)
- Elias Daura-Oller
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Pl. Imperial Tàrraco 1, 43005 Tarragona, Spain
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Applications of Hybrid DFT/Molecular Mechanics to Homogeneous Catalysis. PRINCIPLES AND APPLICATIONS OF DENSITY FUNCTIONAL THEORY IN INORGANIC CHEMISTRY I 2004. [DOI: 10.1007/b97938] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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25
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Granifo J, Garland MT, Baggio R. Stereoisomers of palladium(II) complexes with the dipyridyl ligands 2,3-di(2-pyridyl)pyrazine (dpp), 2,3-di(2-pyridyl)quinoxaline (dpq) and 6,7-dimethyl-2,3-di(2-pyridyl)quinoxaline (ddpq). Crystal structure of [Pd(dpq)2](PF6)2. Inorganica Chim Acta 2003. [DOI: 10.1016/s0020-1693(03)00042-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Heyn RH, Görbitz CH. Synthesis and Molecular Structure of Pd2(C6F5)2[μ-P(C6F5)CH2CH2P(C6F5)2]2. A Rare Example of P−C Bond Cleavage in a Fluoroaryl Phosphine. Organometallics 2002. [DOI: 10.1021/om0200712] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard H. Heyn
- Department of Hydrocarbon Process Chemistry, SINTEF Applied Chemistry, P.O. Box 124 Blindern, N-0314 Oslo, Norway, and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Carl Henrik Görbitz
- Department of Hydrocarbon Process Chemistry, SINTEF Applied Chemistry, P.O. Box 124 Blindern, N-0314 Oslo, Norway, and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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Zuideveld MA, Swennenhuis BHG, Boele MDK, Guari Y, van Strijdonck GPF, Reek JNH, Kamer PCJ, Goubitz K, Fraanje J, Lutz M, Spek AL, van Leeuwen PWNM. The coordination behaviour of large natural bite angle diphosphine ligands towards methyl and 4-cyanophenylpalladium(ii) complexes. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b111596k] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Widhalm M, Nettekoven U, Kalchhauser H, Mereiter K, Calhorda MJ, Félix V. Origin of Enantioselectivity in Palladium-Catalyzed Asymmetric Allylic Alkylation Reactions Using Aminophosphine Ligands. Organometallics 2001. [DOI: 10.1021/om0105369] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Widhalm
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Ulrike Nettekoven
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Hermann Kalchhauser
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Kurt Mereiter
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Maria José Calhorda
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Vítor Félix
- Institut für Organische Chemie, Universität Wien, Währingerstrasse 38, A-1090 Wien, Austria, Institut für Mineralogie, Kristallographie und Strukturchemie, Technische Universität Wien, Getreidemarkt 9, A-1040 Wien, Austria, ITQB, Avenida da República, EAN, Apart. 127, 2781-901 Oeiras, Portugal, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal, and Departamento de Química, Universidade de Aveiro, 3810-193 Aveiro, Portugal
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